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- PDB-6e20: Crystal structure of the Dario rerio galectin-1-L2 -

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Basic information

Entry
Database: PDB / ID: 6.0E+20
TitleCrystal structure of the Dario rerio galectin-1-L2
ComponentsGalectin
KeywordsSUGAR BINDING PROTEIN / Galectin-1 / innate immunity infectious hematopoietic necrosis virus (IHNV) / Danio rerio / zebrafish
Function / homology
Function and homology information


galactoside binding / vasculature development / sprouting angiogenesis / positive regulation of neurogenesis / positive regulation of wound healing / skeletal muscle fiber development / laminin binding / carbohydrate binding / extracellular space / metal ion binding
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
N-acetyl-alpha-lactosamine / Galectin
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGhosh, A. / Bianchet, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R25MH080661 United States
Citation
Journal: Glycobiology / Year: 2019
Title: Structure of the zebrafish galectin-1-L2 and model of its interaction with the infectious hematopoietic necrosis virus (IHNV) envelope glycoprotein.
Authors: Ghosh, A. / Banerjee, A. / Amzel, L.M. / Vasta, G.R. / Bianchet, M.A.
#1: Journal: Proteins / Year: 2000
Title: Soluble beta-galactosyl-binding lectin (galectin) from toad ovary: crystallographic studies of two protein-sugar complexes.
Authors: Bianchet, M.A. / Ahmed, H. / Vasta, G.R. / Amzel, L.M.
#2: Journal: J. Biol. Chem. / Year: 2013
Title: The galectin CvGal1 from the eastern oyster (Crassostrea virginica) binds to blood group A oligosaccharides on the hemocyte surface.
Authors: Feng, C. / Ghosh, A. / Amin, M.N. / Giomarelli, B. / Shridhar, S. / Banerjee, A. / Fernandez-Robledo, J.A. / Bianchet, M.A. / Wang, L.X. / Wilson, I.B. / Vasta, G.R.
#3: Journal: Biochemistry / Year: 2015
Title: Galectin CvGal2 from the Eastern Oyster (Crassostrea virginica) Displays Unique Specificity for ABH Blood Group Oligosaccharides and Differentially Recognizes Sympatric Perkinsus Species.
Authors: Feng, C. / Ghosh, A. / Amin, M.N. / Bachvaroff, T.R. / Tasumi, S. / Pasek, M. / Banerjee, A. / Shridhar, S. / Wang, L.X. / Bianchet, M.A. / Vasta, G.R.
History
DepositionJul 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin
B: Galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6586
Polymers30,8422
Non-polymers8154
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.438, 40.438, 303.639
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Galectin


Mass: 15421.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: lgals2a, lgals1l2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6TGN5
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-lactosamine


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 383.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: N-acetyl-alpha-lactosamine
DescriptorTypeProgram
DGalpb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.2 M Magnesium Chloride Hexahydrate, 30% (v/v) PolyethG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. obs: 18718 / % possible obs: 99.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 33.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 6.5 / Num. unique obs: 1262 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GAN

1gan


Resolution: 2→34.81 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.772 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23405 963 5.1 %RANDOM
Rwork0.17405 ---
obs0.17726 17755 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.813 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20.5 Å2-0 Å2
2--1 Å20 Å2
3----3.25 Å2
Refinement stepCycle: 1 / Resolution: 2→34.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2138 0 54 159 2351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.1130.0132263
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171950
X-RAY DIFFRACTIONr_angle_refined_deg1.8521.683050
X-RAY DIFFRACTIONr_angle_other_deg1.2631.6054576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8185265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10724.274124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39515359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.958158
X-RAY DIFFRACTIONr_chiral_restr0.0690.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022505
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02460
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4123.0581060
X-RAY DIFFRACTIONr_mcbond_other2.4123.0561059
X-RAY DIFFRACTIONr_mcangle_it3.4944.5751322
X-RAY DIFFRACTIONr_mcangle_other3.4934.5771323
X-RAY DIFFRACTIONr_scbond_it2.9843.2921199
X-RAY DIFFRACTIONr_scbond_other2.9843.2921199
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5024.8211728
X-RAY DIFFRACTIONr_long_range_B_refined7.53436.0582372
X-RAY DIFFRACTIONr_long_range_B_other7.32135.9532362
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 71 -
Rwork0.233 1261 -
obs--95.55 %

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